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@@ -1,8 +1,11 @@
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-# The mechanism for directional hearing in fish
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+## The mechanism for directional hearing in fish
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+- [Here](https://www.nature.com/articles/s41586-024-07507-9) you can find the paper.
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+- [Github](https://github.com/danionella/veith_et_al_2024) is your entry point for code.
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+- Click [here](https://danionella.github.io/veith_et_al_2024/) for an interactive online viewer of hearing apparatus anatomy (also on [MorphoSource](http://n2t.net/ark:/87602/m4/623999))
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-This repository contains data related to the manuscript "The mechanism for directional hearing in fish" ([paper](https://www.nature.com/articles/s41586-024-07507-9), [github](https://github.com/danionella/veith_et_al_2024)).
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+This repository contains data related to the manuscript:
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-## Behavior data
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+### Behavior data
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The `behavior` folder contains pickled dataframe objects with fish trajectories around playback events. (5s before playback, 7s after playback, 120fps).
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- `65fish_nolla.zip` Data on 65 female and male adult _Danionella cerebrum_ without lateral line ablation.
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- `74fish_lla.zip` Data on 74 female and male adult _Danionella cerebrum_ after lateral line ablation.
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@@ -17,19 +20,19 @@ https://github.com/danionella/veith_et_al_2024/tree/main/figures
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The subfolder `sleap_model` contains the fish skeleton, parameters, and the trained model that was used to track a single _Danionella cerebrum_ in a 336 x 336 pixel recording, spanning a ~ 11 x 11cm field of view.
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-## Micro CT data
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+### Micro CT data
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PMA (phosphomolybdic acid)-stained, adult, male _Danionella cerebrum_.
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-#### Raw data
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+##### Raw data
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`Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328.raw`
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When opening file in ImageJ Fiji, choose `16-bit Unsigned` and `Little-endian byte order`. Opening as virtual stack is recommended. The voxel size is 1.29702 µm.
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-#### Segmentation (DragonFly)
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+##### Segmentation (DragonFly)
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`Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_segmentation.ORSSession`
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Dragonfly (https://www.theobjects.com/dragonfly) project file, which contains raw data cropped around the inner ear (1224x1224x1645, anchor at 369,246,412), handlabelled planes, interpolated binary ROIs (interpolated by biomedisa, https://biomedisa.info/), and meshgrids derived from these binary ROIs.
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-#### Meshgrids (Blender)
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+##### Meshgrids (Blender)
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`Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_meshgrid.blend`
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This Blender project file contains downsampled meshgrids of segmented inner ear structures and an animation.
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-## Vibrometry data
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+### Vibrometry data
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The `vibrometry` folder contains the reflectance confocal microscope data of auditory structures of two adult male _Danionella cerebrum_ during sound playback. The Matlab code on https://github.com/danionella/veith_et_al_2024/tree/main/figure_3 produces the motion phase maps presented in Fig. 3 and Extended Data Fig. 11 from these data.
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